Update
Browse files- Dockerfile +1 -1
- demo/config.yaml +4 -35
- demo/modules/blocks.py +1 -1
Dockerfile
CHANGED
|
@@ -23,7 +23,7 @@ RUN chmod +x /tmp/foldseek
|
|
| 23 |
RUN huggingface-cli download westlake-repl/ProTrek_650M_UniRef50 --repo-type model --local-dir /tmp/ProTrek_650M_UniRef50
|
| 24 |
|
| 25 |
# Download ProTrek faiss index
|
| 26 |
-
RUN huggingface-cli download westlake-repl/ProTrek-faiss-index --repo-type dataset --local-dir /tmp/
|
| 27 |
|
| 28 |
# Set up a new user named "user" with user ID 1000
|
| 29 |
RUN useradd -m -u 1000 user
|
|
|
|
| 23 |
RUN huggingface-cli download westlake-repl/ProTrek_650M_UniRef50 --repo-type model --local-dir /tmp/ProTrek_650M_UniRef50
|
| 24 |
|
| 25 |
# Download ProTrek faiss index
|
| 26 |
+
RUN huggingface-cli download westlake-repl/ProTrek-faiss-index --repo-type dataset --local-dir /tmp/ProTrek-faiss-index
|
| 27 |
|
| 28 |
# Set up a new user named "user" with user ID 1000
|
| 29 |
RUN useradd -m -u 1000 user
|
demo/config.yaml
CHANGED
|
@@ -1,49 +1,18 @@
|
|
| 1 |
-
model_dir: /
|
| 2 |
faiss_config:
|
| 3 |
IO_FLAG_MMAP: True
|
| 4 |
sequence_index_dir:
|
| 5 |
-
- name: UniRef50
|
| 6 |
-
index_dir: /mnt/5t/faiss_index/UniRef50/ProTrek_650M_UniRef50/sequence
|
| 7 |
- name: Swiss-Prot
|
| 8 |
-
index_dir: /
|
| 9 |
-
- name: PDB
|
| 10 |
-
index_dir: /sujin/Datasets/ProTrek/faiss_index/PDB/ProTrek_650M_UniRef50/sequence
|
| 11 |
-
- name: Uncharacterized
|
| 12 |
-
index_dir: /mnt/5t/faiss_index/Uncharacterized/ProTrek_650M_UniRef50/sequence
|
| 13 |
|
| 14 |
structure_index_dir:
|
| 15 |
- name: Swiss-Prot
|
| 16 |
index_dir: /sujin/Datasets/ProTrek/faiss_index/SwissProt/ProTrek_650M_UniRef50/structure
|
| 17 |
- name: PDB
|
| 18 |
-
index_dir:
|
| 19 |
|
| 20 |
text_index_dir:
|
| 21 |
- name: UniProt
|
| 22 |
index_dir: /mnt/5t/faiss_index/UniRef50/ProTrek_650M_UniRef50/text
|
| 23 |
- name: Swiss-Prot
|
| 24 |
-
index_dir: /
|
| 25 |
-
|
| 26 |
-
#model_dir: /sujin/Models/ProTrek/ProTrek_35M_UniRef50
|
| 27 |
-
#
|
| 28 |
-
#faiss_config:
|
| 29 |
-
# IO_FLAG_MMAP: True
|
| 30 |
-
#
|
| 31 |
-
#sequence_index_dir:
|
| 32 |
-
## - name: UniRef50
|
| 33 |
-
## index_dir: /sujin/Datasets/ProTrek/faiss_index/UniRef50/ProTrek_650M_UniRef50/sequence
|
| 34 |
-
# - name: Swiss-Prot
|
| 35 |
-
# index_dir: /sujin/Datasets/ProTrek/faiss_index/SwissProt/ProTrek_650M_UniRef50/sequence
|
| 36 |
-
## - name: PDB
|
| 37 |
-
## index_dir: /sujin/Datasets/ProTrek/faiss_index/PDB/ProTrek_650M_UniRef50/sequence
|
| 38 |
-
#
|
| 39 |
-
#structure_index_dir:
|
| 40 |
-
# - name: Swiss-Prot
|
| 41 |
-
# index_dir: /sujin/Datasets/ProTrek/faiss_index/SwissProt/ProTrek_650M_UniRef50/structure
|
| 42 |
-
## - name: PDB
|
| 43 |
-
## index_dir: /sujin/Datasets/ProTrek/faiss_index/PDB/ProTrek_650M_UniRef50/structure
|
| 44 |
-
#
|
| 45 |
-
#text_index_dir:
|
| 46 |
-
## - name: UniProt
|
| 47 |
-
## index_dir: /sujin/Datasets/ProTrek/faiss_index/UniRef50/ProTrek_650M_UniRef50/text
|
| 48 |
-
# - name: Swiss-Prot
|
| 49 |
-
# index_dir: /sujin/Datasets/ProTrek/faiss_index/SwissProt/ProTrek_650M_UniRef50/text
|
|
|
|
| 1 |
+
model_dir: /tmp/ProTrek_650M_UniRef50
|
| 2 |
faiss_config:
|
| 3 |
IO_FLAG_MMAP: True
|
| 4 |
sequence_index_dir:
|
|
|
|
|
|
|
| 5 |
- name: Swiss-Prot
|
| 6 |
+
index_dir: /tmp/ProTrek-faiss-index/ProTrek_650M_UniRef50/Swiss-Prot/ProTrek_650M_UniRef50/sequence
|
|
|
|
|
|
|
|
|
|
|
|
|
| 7 |
|
| 8 |
structure_index_dir:
|
| 9 |
- name: Swiss-Prot
|
| 10 |
index_dir: /sujin/Datasets/ProTrek/faiss_index/SwissProt/ProTrek_650M_UniRef50/structure
|
| 11 |
- name: PDB
|
| 12 |
+
index_dir: /tmp/ProTrek-faiss-index/ProTrek_650M_UniRef50/Swiss-Prot/ProTrek_650M_UniRef50/structure
|
| 13 |
|
| 14 |
text_index_dir:
|
| 15 |
- name: UniProt
|
| 16 |
index_dir: /mnt/5t/faiss_index/UniRef50/ProTrek_650M_UniRef50/text
|
| 17 |
- name: Swiss-Prot
|
| 18 |
+
index_dir: /tmp/ProTrek-faiss-index/ProTrek_650M_UniRef50/Swiss-Prot/ProTrek_650M_UniRef50/text
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
demo/modules/blocks.py
CHANGED
|
@@ -42,7 +42,7 @@ def parse_pdb_file(input_type: str, file: str, chain: str) -> str:
|
|
| 42 |
Protein sequence or Foldseek sequence
|
| 43 |
"""
|
| 44 |
try:
|
| 45 |
-
parsed_seqs = get_struc_seq("
|
| 46 |
if input_type == "sequence":
|
| 47 |
return parsed_seqs[0]
|
| 48 |
else:
|
|
|
|
| 42 |
Protein sequence or Foldseek sequence
|
| 43 |
"""
|
| 44 |
try:
|
| 45 |
+
parsed_seqs = get_struc_seq("/tmp/foldseek", file, [chain])[chain]
|
| 46 |
if input_type == "sequence":
|
| 47 |
return parsed_seqs[0]
|
| 48 |
else:
|